SimBPDD_simulation: Simulate Datasets by SimBPDD

In duohongrui/simmethods: A collection of 40+ simulation methods for singlce-cell RNA seqencing data

Simulate Datasets by SimBPDD

Description

This function is used to simulate datasets design_data function in SimBPDD package.

Usage

SimBPDD_simulation(
  ref_data,
  other_prior = NULL,
  return_format,
  verbose = FALSE,
  seed
)

Arguments

ref_data	A matrix for one dataset or a list of datasets with their own names. This is usually unused except for some methods, e.g. SCRIP, SimBPDD, zingeR.
other_prior	A list with names of certain parameters. Some methods need extra parameters to execute the estimation step, so you must input them. In simulation step, the number of cells, genes, groups, batches, the percent of DEGs are usually customed, so before simulating a dataset you must point it out. See Details below for more information.
return_format	A character. Alternatives choices: list, SingleCellExperiment, Seurat, h5ad. If you select h5ad, you will get a path where the .h5ad file saves to.
verbose	Logical. Whether to return messages or not.
seed	A random seed.

Details

In addtion to simulate datasets with default parameters, users want to simulate other kinds of datasets, e.g. a counts matrix with 2 or more cell groups. In SimBPDD, you can set extra parameters to simulate datasets.

The customed parameters you can set are below:

1. nCells. In SimBPDD, you can set nCells directly other_prior = list(nCells = 1000) to simulate 1000 cells.

2. prob.group. You can directly set other_prior = list(prob.group = c(0.4, 0.6)) to assign two proportions of cell groups. Note that the the length of the vector must be 2. For more customed parameters in SimBPDD, please check SimBPDD::bp.sim.DD().

References

Schefzik R. SimBPDD: Simulating differential distributions in Beta-Poisson models, in particular for single-cell RNA sequencing data, Annales Mathematicae et Informaticae, 2021, 53: 283-298. https://doi.org/10.33039/ami.2021.03.003

Github URL: https://github.com/RomanSchefzik/SimBPDD

duohongrui/simmethods documentation built on June 17, 2024, 10:49 a.m.